title: Acute leukemia sample [PT1 DX]

type: genomic

city: MONZA

first: MARTA

last: GALBIATI

address: VIA CADORE

country: Italy

institute: TETTAMANTI RESEARCH CENTER

description: Hybridized to CytoScan HD Array

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
Analysis of copy number variations (CNV) and copy number neutral loss of heterozygosity (cnLOH) regions were performed by Chromosome Analysis Suite software v.3.1.0.15 (Affymetrix®) considering hg19 assembly. Amplifications ≥20kb and deletions ≥15kb, containing a minimum of 20 markers in the region, were considered as significant. Detection of cnLOH was limited to aberrations longer than 2000 kb.
affymetrix-algorithm-name = CYTO2
affymetrix-algorithm-version = 1.15.1
affymetrix-array-type = CytoScanHD_Array
affymetrix-algorithm-param-ArraySet = CytoScanHD_Array
program-name = apt-copynumber-cyto.exe
program-version = 1.15.1

source_name: ALL diagnostic sample

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was isolated using Nuclei Lysis Solution (A7943, Promega, Milano, Italy) and Protein Precipitation Solution (A795, Promega).  DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, and agarose gel electrophoresis.

value: Acute Lymphoblastic Leukemia


title: RNA-seq, Mirg(fl/+) ESC Replicate A

status: Public on Nov 23 2019

type: SRA

city: Cambridge

first: Amanda

last: Whipple

state: MA

address: 16 Divinity Ave

department: Molecular & Cellular Biology

country: USA

institute: Harvard University

description: rRNA-depleted RNA-seq

library_source: transcriptomic

data_processing:
For small RNA-seq and CLIP-seq data, adapter sequences were trimmed using cutadapt (v1.4.2) or fastxtoolkit (v0.0.13).
For CLIP-seq data, reads were collapsed by unique molecular identifier (UMI) and then the UMI was trimmed using fastxtoolkit (v0.0.13).
STAR (v2.4.1d) was used to map sequencing reads to mm10 genome (Gencode M15 assembly) and transcriptome.
RSEM (v1.2.30) was used to count transcriptome mapped reads.
Quantification of RSEM counts was performed using DESeq2.
For CLIP-seq data, biological replicates were merged using samtools. Peaks were called on HA-Ago2 IP sample using CLIPper tool. Then, enrichment for Ago2 binding at each peak was calculated in HA-Ago2 IP samples relative to HA-Ago2 Input and untag-Ago2 IP using seCLIP perl scrips from the Yeo lab (https://github.com/YeoLab/eclip).
Genome_build: mm10
Supplementary_files_format_and_content: mapped reads (STAR output) as bam files, expression values (RSEM output) as tab-delimited text files, and differential gene expression (DESeq2 output) as tab-delimited text files.

molecule: total RNA

organism: Mus musculus

source_name: Embryonic stem cells

growth_protocol: ESCs were grown in ESC medium containing 10% FBS + LIF. iNs were generated by doxycycline-induction of TetO-Ngn2 in neuron differentitiation medium for 10 days.

extract_protocol:
Total RNA was extracted using TRIzol. rRNA-depleted RNA-seq libraries were prepared using KAPA RNA HyperPrep Kit with RiboErase (HMR) (Kapa Biosystems).
rRNA-depleted RNA-sequencing libraries were prepared from 400 ng DNase-treated RNA using KAPA RNA HyperPrep Kit with RiboErase (HMR) (Kapa Biosystems) using 9 cycles of PCR amplification. Quality control on final libraries was assessed with a fragment analyzer and qPCR for colony forming units prior to pooling and loading on an Illumina FlowCell (NextSeq 500, 75 bp PE reads).

tag: cell type

value: Embryonic stem cells

tag: differentiation day

value: Day 0

tag: replicate

value: Replicate A

tag: genotype

value: Mirg(fl/+)


title: RNA-seq, Mirg(Delta/+) ESC Replicate C

description: rRNA-depleted RNA-seq

value: Replicate C

value: Mirg(Delta/+)


title: Acute leukemia sample [PT1 REM]

description: Hybridized to CytoScan HD Array

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: ALL remission sample

tag: tissue


title: P6_9

city: Leipzig

first: Olga

last: Bondareva

state: Saxony

address: Philipp-Rosenthal-Straße 27

department: HI-MAG

country: Germany

institute: Helmholtz Zentrum München

description: scRNA-seq

data_processing:
Raw sequencing data for both single cell and bulk experiments were controlled for quality and trimmed.
For scRNA-seq paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction (Baker et al., 2005). Reads mapping to multiple loci were discarded.
The left read contains the barcode information: the first six bases corresponded to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch. The left read was not used for mapping to the reference transcriptome.
For each cell barcode, the number of UMIs per transcript were counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs were converted into transcript counts (Grün et al., 2014).
Bulk RNA-seq data were mapped to the reference mm10 genome using STAR (Dobin et al., 2013).
The identity of reads was identified through FeatureCount (Liao et al., 2014).
For scRNA-seq analyses, the RNA expression matrices from each cell were merged and further analysed with RaceID3 software package (Herman et al., 2018).
For both scRNA-seq and the bulk Brain-FACS RNA-seq analyses, differentially expressed genes between the cell types or cell clusters were identified using DESeq2 (Love et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited and csv text files include count matrices for scRNA-seq data and bulk RNA-seq samples

source_name: E14.5 brain

extract_protocol:
Mouse E14.5 brain was dissociated and either mCEL-Seq2 protocol for scRNA-seq or population-based FACS-sorting and bulk RNA-seq was performed.
scRNA-seq libraries were prepared according to mCEL-Seq2 protocol. Libraries were sequenced on an Illumina HiSeq 3000 sequencing system (pair-end multiplexing run, high output mode) at a depth of ~200,000 reads per cell. Population-based FACS-sorting and bulk RNA-seq  from neural cells was isolated using the Qiagen mini kit (#74104), while RNA from mural cells, endothelial cells and microglia was extracted using the Qiagen miRNeasy Micro kit (#1071023). Libraries for RNA-seq of the neural population were prepared using the Illumina TruSeq library preparation kit. For mural cells, endothelial cells and microglia, cDNA was prepared from isolated RNA using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech 634891). Libraries were prepared using the Nextera XT DNA library preparation kit (Illumina FC-131-1096) and sequenced on the HiSeq 2500 instrument.
scRNA-seq

value: Mof Knockout


title: P5_8

description: scRNA-seq


title: Liver, SHAM+GW rep3

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

data_processing:
reads were pre-processed to remove any adapater sequences and quality trimmed (<20) with Trimmomatic 0.39
reads were mapped to the reference using the hisat2 (v 2.1.0) aligner and using the mm10 version of the mouse genome and the ensembl 92 genome annotation (with extra options “--rna-strandness R -p 4”)
featureCounts (v 1.6.2) was used to obtain read counts per gene (with extra options: “-Q 10 --primary -T 3")
differential gene expression was determined using the DESeq2 R packagewith pairwise comparisons, we corrected for multiple testing using the Benjamini–Hochberg method
Genome_build: mm10
Supplementary_files_format_and_content: tab separated text file containing read counts (not normalized) per gene for every sample; output from fearureCounts

source_name: liver

extract_protocol:
RNA isolation was done with the Aurum™ Total RNA Mini Kit (Bio-Rad) according to the manufacturers protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CLP or SHAM operation followed by administration of GW7647 (20µg/g) or DMSO after 6h, organ isolation following 4h after (total: 10h)

tag: strain

value: liver

tag: age

value: 8 weeks

tag: operation

value: SHS

tag: treatment

value: GW7647 (PPARα agonist)


title: Liver, SHAM+GW rep2


title: P5_7

description: scRNA-seq


title: Liver, SHAM+GW rep1


title: Liver, SHAM+DMSO rep2

value: DMSO


title: P5_6

description: scRNA-seq


title: P5_5

description: scRNA-seq


title: Liver, SHAM+DMSO rep3


title: Liver, SHAM+DMSO rep1


title: P4_4

description: scRNA-seq


title: P4_2

description: scRNA-seq


title: Liver, CLP+GW rep3

value: CLP


title: P4_3

description: scRNA-seq


title: Liver, CLP+DMSO rep3


title: Liver, CLP+DMSO rep2


title: Liver, CLP+GW rep1


title: P4_1

description: scRNA-seq


title: HAND13_T16

type: RNA

city: Granada

first: Jorge

last: Molina

state: Granada

address: Campus de la Cartuja S/N

department: Physiology

country: Spain

institute: University of Granada

description:
Handball athlete
SAMPLE 78

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software Expression Suite for QuantStudio 12K Flex Real-Time PCR System (Applied Biosystems, Thermo Fisher Scientific, Carlsbad, CA, USA). http://sabiosciences.com/pcrarraydataanalysis.php
A total of 52 genes were included in the analysis in order to determine the stability value (M) and the coefficient of variation of the normalized reference gene expression levels using qBasePLUS software (Biogazelle, Gent, Belgium).
The selected housekeeping genes were: ATP5B (ATP synthase H+ transporting, mitochondrial F1 complex, beta polypeptide; NC_000076.6; gene expression assay Hs00969569_m1, Applied Biosystems); LUC7L2 (LUC7 like 2, pre-RNA splicing factor; NC_000007.14; gene expression assay Hs00255388_m1, Applied Biosystems); ARF1 (ADP-ribosylation factor 1; NC_000001.11; gene expression assay Hs00734523_m1, Applied Biosystems); and PAPOLA (Poly(A) polymerase alpha; NC_000014.9; gene expression assay Hs00413685_m1, Applied Biosystems). The mean of the housekeeping genes to use as the value for normalization.
Target gene signals normalized to housekeeping genes, where deltaCt = (Ct_Target − Ct_HKG)]

label: Taqman

source_name: Total blood samples

label_protocol: Reverse transcription was performed with random hexamers using the High Capacity cDNA Reverse Transcription Kit (Life Technologies, Carlsbad, CA, USA) according to the instructions of the manufacturer. Two μg of the total RNA was reverse transcribed with random hexamers using the High Capacity cDNA Reverse Transcription Kit. Thermal cycler conditions were set to run for two hours at 37°C and for 10 minutes at 75°C, followed by rapid cooling to 4°C.

extract_protocol: Total RNA was extracted with PAXgene blood RNA tube (Becton Dickinson, Germany) by DNase I treatment. The RNA yield was estimated by measuring absorbance at 260 nm in a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific). RNA purity was calculated from the ratio of absorbance at 260 nm and 280 nm. The OD 260/280 ratio was between 1.9 and 2.2 for all samples. RNA integrity was assessed using the Eukaryote Total RNA Nano assay on an Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: subject id

value: Total blood

tag: activation agent

value: Experimental group

tag: time

value: T16 (after 16 weeks in absence to supplement)


title: Liver, CLP+DMSO rep1


title: EX18_17_18_DILI-T7D-03_47

first: Jordi

last: Martorell-Marugan

address: Avenida de la Ilustración 114

department: Bioinformatics Unit

institute: GENyO

data_processing:
bcl2fastq v2.18.0.12 used for basecalling
Raw sequences were trimmed in order to remove adapter sequences and random nucleotides introduced during the library preparation.
Reads shorter than 15 nucleotides (nt) and larger than 28 nt after trimming were discarded.
We used QuickMIRSeq to map not only against reference miRNAs, but also against possible isomiRs with length variations of ± 4 nucleotides at the 5' end and ± 5 nucleotides at the 3' end.
Genome_build: GRCh38
Supplementary_files_format_and_content: Text file with reads-per-million (RPM) counts for each isomiR (rows) and all samples (columns)

source_name: serum from DILI patient

extract_protocol:
microRNA was extracted using a miRNeasy Serum/Plasma kit [Qiagen, Venlo,Netherlands] following the manufacturer’s instructions. Total RNA was extracted from 50 μL of serum diluted in 150 μL nuclease free water. Briefly, RNA was extracted from the serum by lysis reagent [1000 μL] and chloroform [200 μL]. After centrifugation at12,000 x g for 15 min at 4°C up to 600 μL of the aqueous phase was transferred to a newtube with 900 μL absolute ethanol. RNA was purified on an RNeasy minElute spincolumn and eluted in 15 μL RNase-free water and stored at -80°C. Extraction efficiency was monitored by adding 5.6 x 108 copies of synthetic C.elegans miR-39 spike-in controlafter the addition of lysis reagent before the addition of chloroform and phaseseparation.
Standard quality control steps were included to determine total RNA quantity and quality using Agilent 2100 Bioanalyzer with Eukaryote Total RNA Pico Kit and High Sensitivity DNA Assay (AgilentTechnologies, Santa Clara, CA). Libraries were prepared using the TruSeq StrandedmRNA Library preparation Kit (Illumina Inc., San Diego, USA).

value: serum

value: 7 days


title: EX18_17_17_DILI-T7D-02_46


title: EX18_17_15_HEALTHY-T7D-03_44

source_name: serum from healthy control


title: HAND9_T16

description:
Handball athlete
SAMPLE 74


title: EX18_17_14_HEALTHY-T7D-02_43


title: EX18_17_16_DILI-T7D-01_45


title: HAND12_T16

description:
Handball athlete
SAMPLE 77


title: HAND11_T16

description:
Handball athlete
SAMPLE 76


title: HAND7_T16

description:
Handball athlete
SAMPLE 72


title: HAND6_T16

description:
Handball athlete
SAMPLE 71


title: HAND8_T16

description:
Handball athlete
SAMPLE 73


title: HAND10_T16

description:
Handball athlete
SAMPLE 75


title: EX18_17_13_HEALTHY-T7D-01_42


title: EX18_17_11_DILI-T24H-02_40

value: 24 hours


title: Liver, CLP+GW rep2


title: HAND5_T16

description:
Handball athlete
SAMPLE 70


title: EX18_17_10_DILI-T24H-01_39


title: HAND2_T16

description:
Handball athlete
SAMPLE 67


title: HAND4_T16

description:
Handball athlete
SAMPLE 69


title: EX18_17_09_HEALTHY-T24H-03_38


title: EX18_17_08_HEALTHY-T24H-02_37


title: SED13_T16

description:
Sedentary
SAMPLE 65

value: Control group


title: EX18_17_06_DILI-T0-03_34


title: EX18_17_05_DILI-T0-02_33


title: EX18_17_07_HEALTHY-T24H-01_35


title: EX18_17_03_HEALTHY-T0-03_31


title: SED11_T16

description:
Sedentary
SAMPLE 63


title: EX18_17_04_DILI-T0-01_32


title: SED12_T16

description:
Sedentary
SAMPLE 64


title: EX18_17_02_HEALTHY-T0-02_30


title: EX18_17_12_DILI-T24H-03_41


title: EX18_17_01_HEALTHY-T0-01_29


title: HAND3_T16

description:
Handball athlete
SAMPLE 68


title: SED9_T16

description:
Sedentary
SAMPLE 61


title: SED8_T16

description:
Sedentary
SAMPLE 60


title: SED7_T16

description:
Sedentary
SAMPLE 59


title: SED6_T16

description:
Sedentary
SAMPLE 58


title: VP-Pt9-CD34

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

description: processed data file: RawCounts.csv

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Sequenced reads were mapped to GRCh38 reference GENCODE annotation (p7) using tophat 2.0.13.
TopHat aligned BAMs were merged using MergeSamFiles from Picard v1.97.
Reads counts are obtained using HTSeq v0.6.1 using intersect-strict option.
Genome_build: GRCh38
Supplementary_files_format_and_content: RawCounts.csv: Comma-separated text file includes raw counts.

source_name: bone marrow cells

extract_protocol:
< 100 cells were directly sorted into PCR tubes containing 9.5 µL of PBS.
RNA-seq libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio USA, Inc.). Briefly, the cells were lysed and first-strand cDNA was synthesized utilizing template switching oligos. Amplified double stranded cDNA was created by PCR using blocked PCR primers. The resulting cDNA was purified using AmpureXP beads (Beckman Coulter, Inc). Purified cDNA was quantitated by Qubit hs DNA (Thermo Fisher Scientific, Inc.) and 1ng of material was used for subsequent library generation utilizing Nextera XT reagents (Illumina, Inc). Tagmentation was performed to shear the full length cDNA to the appropriate size and incorporate partial adapter sequences. 12 cycles of PCR using Nextera XT primers complete the library and incorporate unique sample barcodes. The final libraries were purified using AmpureXP beads, and validated for appropriate size on a 4200 TapeStation D1000 Screentape (Agilent Technologies, Inc.).
The DNA libraries were quantitated using KAPA Biosystems qPCR kit, and were pooled together in an equimolar fashion.  Each pool was denatured and diluted to 2.4pM with 1% PhiX control library added.  The resulting pool was then loaded into the NextSeq 150 cycle high output reagent cartridge, and sequenced on a NextSeq500 following the manufacturer’s recommended protocol (Illumina, Inc.).

tag: disease status

value: Myelodysplastic syndrome


title: VP-Pt9-CD1c

description: processed data file: RawCounts.csv


title: VP-Pt7-pre-CD34

description: processed data file: RawCounts.csv


title: SED10_T16

description:
Sedentary
SAMPLE 62


title: SED4_T16

description:
Sedentary
SAMPLE 56


title: VP-Pt9-CD141Hi

description: processed data file: RawCounts.csv


title: SED1_T16

description:
Sedentary
SAMPLE 53


title: SED5_T16

description:
Sedentary
SAMPLE 57


title: SED2_T16

description:
Sedentary
SAMPLE 54


title: HAND1_T16

description:
Handball athlete
SAMPLE 66


title: VP-Pt7-pre-CD1c

description: processed data file: RawCounts.csv


title: Condition 3-2

city: Bogotá

first: Albert

middle: Enrique

last: Tafur Rangel

address: Cra 1 Nº 18A - 12 Edificio ML

department: Chemical and Food Engineering

country: Colombia

institute: Universidad de Los Andes

description:
processed data file: Supplementary_file_S1.xlsx
Supplementary_file_S1.xlsx: Column Con_3_2

data_processing:
Evaluate sequence quality.
Trimm reads by using trimmomatic v 0.38.
Map reads to genome RefSeq Escherichia coli ATCC 8739 using bowtie2.
Counts by using featureCounts.
SARTools (Statistical Analysis of RNA-Seq data Tools) was used for statistical RNA-Seq analysis. Differentially expressed genes (DEGs) were identified by using the DESeq2 R Package.
Genome_build: NC_010468.1
Supplementary_files_format_and_content: Supplementary_file_S1.xlsx: Excel file with normalized counts and differential expression.

organism: Escherichia coli

source_name: bacterial total RNA

growth_protocol: To compare the global gene expression profiles between cells grown in an optimized culture medium (condition 3) and one evolved strain. Triplicates of E. coli ATCC 8739 were grown in a glycerol-based medium containing 5 g/L yeast extract, 2.5 g/L NaCl, 5mL/L trace metals solution (0.55 g/L CaCl2, 0.10 g/L MnCl2 4H2O, 0.17 g/L ZnCl2, 0.043 g/L CuCl2 2H2O, 0.06 g/L CoCl2 6H2O, 0.06 g/L Na2MoO4 2H2O, 0.06 g/L Fe(NH4)2(SO4)2 6H2O, 0.20 g/L FeCl3 6H2O), 5 mL/L MgSO4 1M, 30 g/L glycerol for the reference conditions (Condition 11). Condition 3 and evolved strain were grown in triplicates in the glycerol-based medium supplemented with 1g/L of NH4Cl, 6 g/L of Na2HPO4, and 3 g/L of K2HPO4. All the cultures were carried out at 37°C and 200 rpm in 250 ballfed Erlenmeyer containing 50 ml of culture medium.

extract_protocol:
The Qiagen RNeasy Mini kit (Cat No./ID: 74104) was used to obtain total RNA for further analysis according to the manufacturer’s protocol. Each sample was treated with DNase in order to remove the genomic DNA.
Genewiz protocol. Whole transcriptome sequencing via rRNA depletion.

treatment_protocol: In order to harvest the cells to purify RNA after six h of culture, sample were first treated with RNAprotect bacterial reagent (Cat No./ID: 76506) and enzymatic lysis and Proteinase K digestion of bacteria was carried out following the manufacturer’s protocol.

value: ATCC 8739


title: HAND13_T8

description:
Handball athlete
SAMPLE 52

value: T8 (after 8 weeks of supplement)


title: VP-Pt7-pre-CD141Hi

description: processed data file: RawCounts.csv


title: SED3_T16

description:
Sedentary
SAMPLE 55


title: VP-Pt6-pre-CD34

description: processed data file: RawCounts.csv


title: HAND12_T8

description:
Handball athlete
SAMPLE 51


title: VP-Pt6-pre-CD141Hi

description: processed data file: RawCounts.csv


title: VP-Pt2-pre-CD34

description: processed data file: RawCounts.csv


title: VP-Pt6-pre-CD1c

description: processed data file: RawCounts.csv


title: HAND11_T8

description:
Handball athlete
SAMPLE 50


title: VP-Pt1-pre-CD34

description: processed data file: RawCounts.csv


title: VP-Pt2-pre-CD1c

description: processed data file: RawCounts.csv


title: VP-Pt1-pre-CD1c

description: processed data file: RawCounts.csv


title: HAND10_T8

description:
Handball athlete
SAMPLE 49


title: HAND8_T8

description:
Handball athlete
SAMPLE 47


title: HAND7_T8

description:
Handball athlete
SAMPLE 46


title: HAND5_T8

description:
Handball athlete
SAMPLE 44


title: HAND6_T8

description:
Handball athlete
SAMPLE 45


title: HAND4_T8

description:
Handball athlete
SAMPLE 43


title: NBM-9-CD1c

description: processed data file: RawCounts.csv

value: Healthy donor


title: NBM-9-CD34

description: processed data file: RawCounts.csv


title: HAND3_T8

description:
Handball athlete
SAMPLE 42


title: HAND2_T8

description:
Handball athlete
SAMPLE 41


title: HAND1_T8

description:
Handball athlete
SAMPLE 40


title: NBM-9-CD141Hi

description: processed data file: RawCounts.csv


title: SED13_T8

description:
Sedentary
SAMPLE 39


title: NBM-7-CD34

description: processed data file: RawCounts.csv


title: VP-Pt2-pre-CD141Hi

description: processed data file: RawCounts.csv


title: HAND9_T8

description:
Handball athlete
SAMPLE 48


title: SED12_T8

description:
Sedentary
SAMPLE 38


title: SED11_T8

description:
Sedentary
SAMPLE 37


title: NBM-7-CD1c

description: processed data file: RawCounts.csv


title: SED10_T8

description:
Sedentary
SAMPLE 36


title: SED8_T8

description:
Sedentary
SAMPLE 34


title: SED9_T8

description:
Sedentary
SAMPLE 35


title: SED7_T8

description:
Sedentary
SAMPLE 33


title: SED6_T8

description:
Sedentary
SAMPLE 32


title: NBM-6-CD34

description: processed data file: RawCounts.csv


title: RA04

city: New Haven

first: Kofi

last: Mensah

state: CT

address: 300 George Street

department: Rheumatology, Allergy and Clinical Immunology

institute: Yale University School of Medicine

hyb_protocol: Targets were prepared for array hybridization according to Affymetrix Expression Analysis Technical manual except for some modifications. Hybridization conditions, array washing and staining (with GeneChip Fluidics Station 450) were carried out according to the Affymetrix Expression Analysis technical Manual.

scan_protocol: Scanning (with GeneChip Scanner 3000 7G) was carried out according to the Affymetrix Expression Analysis technical Manual. Pixel Size 1.56. Filter 570. Scanner ID  50207250. Number of Scans 1. Scanner Type M10

data_processing: Affymetrix GeneChip Operating Software was used as the image acquisition software for the U133A 2.0 chips. The signal, which represents the intensity of each gene, was extracted from the image. The target intensity value from each chip was scaled to 500.

source_name: CD19+CD21+CD10-CD27- naïve B cells

label_protocol: 50 ng of total RNA were amplified and labeled with biotin using the Ovation Biotin system (NuGEN Technologies, Inc., San Carlos, CA). Single stranded cDNA amplified from total RNA was then fragmented and labeled with biotin.

extract_protocol: Total RNA was extracted from 300,000 cells and purified using the AbsolutelyRNA microprep kit from Stratagene, by following the manufacturer’s protocol. Prior to use in amplification studies, the size integrity profile of all RNA samples was determined with an Agilent Bioanalyzer. All RNA preparation provided (A260/280) ratios greater than 1.8. RNA concentration was determined by Nanodrop spectrophotometry.

treatment_protocol: Peripheral B cells were purified from the blood of the donor by negative selection using RosetteSepTM procedure (StemCell Technologies, Vancouver, BC, Canada). Enriched B cells were stained with FITC anti-human CD27, PE anti-human CD10, PECy7 anti-human CD19, and APC anti-human CD21. Single CD19+CD21+CD10-CD27- mature naive from the donor were sorted on a FACSVantage (Becton Deckinson).

tag: diagnosis

value: Rheumatoid arthritis patient

value: CD19+CD21+CD10-CD27- naïve B cells


title: SED5_T8

description:
Sedentary
SAMPLE 31


title: RA22


title: SED4_T8

description:
Sedentary
SAMPLE 30


title: NBM-6-CD1c

description: processed data file: RawCounts.csv


title: SED3_T8

description:
Sedentary
SAMPLE 29


title: RA20


title: SED2_T8

description:
Sedentary
SAMPLE 28


title: RA27


title: NBM-4-CD34

description: processed data file: RawCounts.csv


title: hlh-11 OE rep2

city: beijing

first: Yi

last: Li

state: beijing

address: peking univerity, haidian district

country: China

institute: PKU

data_processing:
Perform pre-mapping sequencing quality evaluation using FastQC [v0.11.5] on clean data.
The clean reads were aligned to WBcel235 genomes with tophat2 [version: VN: 2.1.1; main parameters: --min-anchor-length 8 -N 6 --read-edit-dist 6 --read-realign-edit-dist 3 --segment-length 30].
Gene expressions were obtained with in-house perl script [geneRPKM.pl] and WBcel235 annotations v87.
Gene differential expression analysis was performed using DEseq2. p < 0.05
Genome_build: WBcel235 release 87

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: Worms were grown on standard nematode growth medium(NGM) plates with E. coli OP50 at 20 °C using standard protocols.

extract_protocol:
For each sample, approximately 2,000 synchronized young adult worms were collected and resuspended in TRIzon Reagent(CW0580, CWBIO). Total RNA was isolated by chloroform extraction, followed by isopropanol precipitation.
RNA libraries were prepared for sequencing using standard Illumina protocols. PolyA RNA was selected.

tag: genotype/variation

value: hlh-11 over-expression

tag: Stage

value: Young adult


title: hlh-11 OE rep1


title: HAND12_T0

description:
Handball athlete
SAMPLE 25

value: T0 (baseline)


title: NBM-4-CD1c

description: processed data file: RawCounts.csv


title: HAND13_T0

description:
Handball athlete
SAMPLE 26


title: NBM-7-CD141Hi

description: processed data file: RawCounts.csv


title: RA24


title: HAND11_T0

description:
Handball athlete
SAMPLE 24


title: RA01


title: RA14


title: hlh-11 KO rep2

value: hlh-11 knock-out


title: NBM-4-CD141Hi

description: processed data file: RawCounts.csv


title: hlh-11 KO rep1


title: NBM-2-CD34

description: processed data file: RawCounts.csv


title: NBM-6-CD141Hi

description: processed data file: RawCounts.csv


title: HAND7_T0

description:
Handball athlete
SAMPLE 20

value: Total blood


title: WT rep2

value: wild type


title: SED1_T8

description:
Sedentary
SAMPLE 27


title: WT rep1


title: NBM-2-CD141Hi

description: processed data file: RawCounts.csv


title: NBM-11-CD34

description: processed data file: RawCounts.csv


title: HAND5_T0

description:
Handball athlete
SAMPLE 18

value: Experimental group


title: HAND6_T0

description:
Handball athlete
SAMPLE 19


title: HCV-HCC-T3: Tumor Liver tissue (Total RNA-Seq)

city: Kolkata

first: Soma

last: Banerjee

state: West Bengal

address: 244, A.J.C Bose Road

department: School of Digestive & Liver Diseases

country: India

institute: Institute of Post Graduate Medical Education & Research

description:
Tumor tissue from orthotropic liver transplant of HCV infected HCC patients
HCCT3

data_processing:
The adapter trimming was performed using fastq-mcf program (version - 1.04.676) and cutadapt version 1.8dev.
The paired-end reads were aligned to the reference human genome downloaded from UCSC database (GRCh37/hg19) as released on February 2009.
Alignment was performed using HISAT (a fast spliced aligner with low memory requirements) program (version 0.1.7).
The aligned reads were used for coverage analysis of the genes and transcripts (or mRNAs) using program HTSeq-0.6.1.
The Differential expression analysis was performed using DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: Sequence Total RNA_normalized.xlsx

source_name: Liver Tissue

extract_protocol:
About 5 mg of liver tissues were powdered keeping frozen in liquid nitrogen and the total RNA was isolated using TRIzol (Invitrogen, CA) following the manufacturer's protocol. Quality of each RNA was verified using Bioanalyzer (Agilent, CA) and RNA integrity number (RIN) ≥5.5 was considered for Next Generation Sequencing (NGS).
Samples with RIN value more than 5.5 were subjected to high throughput total RNA sequence analysis in Medgenome private limited, Bangalore, India using Illumina Hiseq2500 platform. Total RNA isolated from each of five normal and five HCV-HCC were first depleted of cytoplasmic and mitochondrial rRNA by Truseq Ribo Zero Gold Kit (Illumina) and then purified RNAs were fragmented. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products were purified and enriched with PCR to create the final cDNA library. It was then subjected to sequencing on Illumina Platform HiSeq 2500.

value: HCC Tumor Tissue

tag: etiology

value: HCV

tag: gender

value: Male


title: HCV-HCC-T4: Tumor Liver tissue (Total RNA-Seq)

description:
Tumor tissue from orthotropic liver transplant of HCV infected HCC patients
HCCT4


title: HAND10_T0

description:
Handball athlete
SAMPLE 23


title: HAND9_T0

description:
Handball athlete
SAMPLE 22


title: HAND1_T0

description:
Handball athlete
SAMPLE 14


title: HAND3_T0

description:
Handball athlete
SAMPLE 16


title: HAND8_T0

description:
Handball athlete
SAMPLE 21


title: NBM-11-CD1c

description: processed data file: RawCounts.csv

tag: cell type


title: NBM-11-CD141Hi

description: processed data file: RawCounts.csv


title: SED10_T0

description:
Sedentary
SAMPLE 10

value: Control group


title: NBM-2-CD1c

description: processed data file: RawCounts.csv


title: SED9_T0

description:
Sedentary
SAMPLE 9


title: RA29


title: HAND4_T0

description:
Handball athlete
SAMPLE 17


title: SED13_T0

description:
Sedentary
SAMPLE 13


title: SED12_T0

description:
Sedentary
SAMPLE 12


title: HCV-HCC-T1: Tumor Liver tissue (Total RNA-Seq)

description:
Tumor tissue from orthotropic liver transplant of HCV infected HCC patients
HCCT1


title: HCV-HCC-T2: Tumor Liver tissue (Total RNA-Seq)

description:
Tumor tissue from orthotropic liver transplant of HCV infected HCC patients
CLR2-HCC-T2


title: SED8_T0

description:
Sedentary
SAMPLE 8


title: 15: Atg16L1 dIEC TNFa 3

city: New York

first: Yu

last: Matsuzawa

address: 430 East 29th Street, 4th Floor, Lab 424

institute: New York University School of Medicine

data_processing: Aligned RNA was analyzed for fold change. Sequencing data were processed using the Tuxedo suite; reads were aligned with TopHat v2.1.1 against UCSC mm10 genome assembly and normalized read counts were calculated using Cufflinks v2.2.1 against the same reference genome. Differential gene expression was determined with Cuffdiff and gene ontology analysis performed using Qiagen’s Ingenuity Pathway Analysis (IPA, QIAGEN)

source_name: small intestinal organoids

growth_protocol: Small intestinal crypts were isolated and cultured for 3 days according to our previous study ( Matsuzawa-Ishimoto et al. J Exp Med 2017).

extract_protocol:
Total RNA was extracted using TRIzol (ThermoFisher) according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Organoids were treated with 20 ng/ml murine TNFa for 2 hours.

tag: tag

value: small intestinal organoids

value: Day 3, TNFa stimulation for 2hr


title: SED7_T0

description:
Sedentary
SAMPLE 7


title: HN5: Uninfected Normal Liver tissue (Total RNA-Seq)

description:
Normal Liver Tissue from Gall Bladdar Carcinoma patients after histological verification
CLR2-HN5

value: Normal Liver Tissue

value: Uninfected


title: SED6_T0

description:
Sedentary
SAMPLE 6


title: SED5_T0

description:
Sedentary
SAMPLE 5


title: 14: Atg16L1 dIEC TNFa 2


title: SED3_T0

description:
Sedentary
SAMPLE 3


title: 16: Atg16L1 dIEC TNFa 4


title: 12: Atg16L1 f/f TNFa 4


title: 11: Atg16L1 f/f TNFa 3


title: HN2: Uninfected Normal Liver tissue (Total RNA-Seq)

description:
Normal Liver Tissue from Gall Bladdar Carcinoma patients after histological verification
CLR2-HN2


title: 13: Atg16L1 dIEC TNFa 1


title: HN1: Uninfected Normal Liver tissue (Total RNA-Seq)

description:
Normal Liver Tissue from Gall Bladdar Carcinoma patients after histological verification
HN1


title: SED1_T0

description:
Sedentary
SAMPLE 1


title: 8: Atg16L1 dIEC 4

value: Day 3, no stimulation


title: 10: Atg16L1 f/f TNFa 2


title: TNF-alpha + ACSL3 siRNA 2

city: SEATTLE

first: KARIN E

last: BORNFELDT

state: WA

address: 750 Republican St

institute: UNIV WASHINGTON

data_processing:
Massively parallel sequencing-by-synthesis with fluorescently labeled, reversibly terminating nucleotides was carried out on the HiSeq sequencer at the Northwest Genomics Center at the University of Washington. The processing pipeline consisted of the following elements: (1) base calls generated in real-time on a HiSeq4000 instrument (RTA 2.7.6); (2) demultiplexed, unaligned BAM files produced by Picard ExtractIlluminaBarcodes and IlluminaBasecallsToSam were converted to FASTQ format using SamTools bam2fq (v1.4); (3) sequence read and base quality were confirmed using the FASTX-toolkit (v0.0.13); (4) sequences were aligned to GRCh38 with reference transcriptome GENCODE release 26 (GRCh38.p10) using STAR (v2.5.3a). Transcript-level expression quantification was generated with RNA-SeQC (v1.1.9) and RSEM (v1.3.0). RPKM (reads per kilo base per million mapped reads) and TPM  (transcripts per kilobase million) for transcript isoforms were quantitated on the merged lane-level data with RSEM (v1.3.0). Gene-level RPKMs were quantitated with RNA-SeQC (v1.1.9) on a standard collapsed reference annotation.  Key expression quality control metrics were reviewed for outliers. Marginal outliers in quality were identified using the interquartile ranges (IQR; ~1.5 * IQR) and flagged for further review. PCA plots of meta data were generated using PCA analysis and were colored and visualized using standard PCA plotting packages in Python for detection of confounding effects. Differential expression from RNA-seq experiments was determined for TPM, normalizing for gene length and sequencing depth.
Genome_build: GRCh38 with reference transcriptome GENCODE release 26 (GRCh38.p10)
Supplementary_files_format_and_content: transcriptome_hits.merged.genes.results and transcriptome_hits.merged.isoforms.results

source_name: Cultured endothelial cells

growth_protocol: Human coronary artery endothelial cells from a 40-year old woman donor (LifeLine Cell Technology) were grown in VascuLife® VEGF Endothelial Medium (LL-0003, LifeLine Cell Technology) and used at passages 5-9. For experiments, the medium was replaced with medium without FGF, IGF and VEGF for 4 h before the stimulation with human TNF-α (20 ng/ml, PeproTech Inc.).

extract_protocol:
NucleoSpin RNA plus
For library production, total RNA was normalized to 10 ng/uL in a total volume of 50 uL on a Perkin Elmer Janus Workstation (Perkin Elmer, Janus II).  Poly-A selection and cDNA synthesis were performed using the TruSeq Stranded mRNA kit as outlined by the manufacturer (Illumina, cat#RS-122-2103).  All steps were automated on the Perkin Elmer Sciclone NGSx Workstation to reduce batch to batch variability and to increase sample throughput.  Final RNASeq libraries were quantified using the Quant-it dsDNA High Sensitivity assay, and library insert size distribution was confirmed using a fragment analyzer (Advanced Analytical; kit ID DNF474).  Samples where adapter dimers constitute more than 4% of the electopherogram area were failed prior to sequencing.  Technical controls (K562,Thermo Fisher Scientific, cat# AM7832), were compared to expected results to ensure that batch to batch variability was minimized.  Successful libraries were normalized to 10 nM for submission to sequencing. Barcoded libraries were pooled using liquid handling robotics prior to clustering (Illumina cBot) and loading.

treatment_protocol: Human coronary artery endothelial cells were electroporated in the presence of control siRNA (negative control #2; 300 nM; Ambion) or ACSL3 siRNA (s4997; 300 nM; Ambion), recovered for 72 h, and then stimulated with and without TNF-alpha (20 ng/ml) for 18 h.

value: Human coronary artery endothelial cells

value: Female

value: 40 yrs

tag: sirna

value: TNF-alpha + ACSL3 siRNA


title: TNF-alpha + ACSL3 siRNA 3


title: HAND2_T0

description:
Handball athlete
SAMPLE 15

tag: tissue

value: T0 (baseline)


title: HCV-HCC-T5: Tumor Liver tissue (Total RNA-Seq)

description:
Tumor tissue from orthotropic liver transplant of HCV infected HCC patients
HCCT5


title: TNF-alpha + ACSL3 siRNA 1


title: 7: Atg16L1 dIEC 3


title: 56CON_re-used

city: Boston

first: Annie

last: Kathuria

address: 185 cambridge street

institute: Mass Gen Hospital

description:
sample_29
GSM3954333

data_processing:
Analysis was performed by DNA Link USA, Inc.
Sequence quality was assessed using FASTQC
Sequences were trimmed using cutadapt v 1.18, paired-end reads mode -u 7 -u -3 -U 7 -U -3
Trimmed reads were aligned to the reference genome using TopHat v2.1.1 (--no-coverage-search, -G refseqhg38p9.gtf)
Bam files were merged using samptools v 1.9 for samples with techincal replicates.
FPKM calulcation done using cufflinks v2.2.1 using annotation from RefSeq assembly hg38 p9 which was modified according UCSC-style-name
Pairwise differential expression analysis was performed using cuffdiff v2.2.1
Genome_build: Homo sapience hg38 (UCSC tophat version as downloaded May 2017)
Supplementary_files_format_and_content: tab-delimited w/ the following columns: tracking_id, gene_id, gene_short_name, locus, FPKM for each sample

source_name: cerebral organoids

extract_protocol:
Tissue was dissolved in Trizol and RNA was extracted using qiagen rneasy kit
RNA libraries were prepared for sequencing using Truseq Stranded Total RNA H/M/R

value: Human iPSC derieved cerebral organoids

value: 6 months of differentiation

value: healthy control


title: TUBE FORMATION 6

city: TUCSON

first: Ravi

last: Goyal

state: Arizona

address: 1501 N. Campbell Ave

institute: University of Arizona

hyb_protocol: 1 µg of purified cRNA was fragmented to a uniform size and then applied to the microarray chips. Microarray chips baked for 17 hours at 65° C in a shaking incubator.

scan_protocol: Following hybridization, the chips were washed at 37° C for 1 min. The chips were dried and then scanned at 5 µm resolution with an G2565 Microarray Scanner from Agilent Technologies.

data_processing: Scanned images from the arrays were processed to conduct gridding and intensity extraction by Feature Extraction software from Agilent. The data obtained was further analyzed by using GeneSpring GX v7.3.1 software (Agilent Technologies).

source_name: CELL SYSTEMS REPOSITORY

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1  ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Trizol method was used to isolate RNA. RNA purity was assessed by measuring the absorbance at OD260/280, and the RNA with value between 1.8 and 2.0 were included in the study. The RNA quality and fragmentation were examined using an Agilent. Bioanalyzer

treatment_protocol: HBMECs were plated on growth factor reduced basal matrix extract (Corning™ Basal matrix extract™ Membrane Matrix GFR, Cat # CB-40230, Fisher Scientific, Hampton, NH). Tube formation was complete by 16-24 hours.

value: PRIMARY CELLS

tag: group

value: tube formation


title: TUBE FORMATION 5


title: SED4_T0

description:
Sedentary
SAMPLE 4

value: Total blood


title: 6: Atg16L1 dIEC 2


title: HN3: Uninfected Normal Liver tissue (Total RNA-Seq)

description:
Normal Liver Tissue from Gall Bladdar Carcinoma patients after histological verification
CLR2-HN3

value: Male


title: Basal + ACSL3 siRNA 3

tag: age

value: Basal + ACSL3 siRNA


title: 9: Atg16L1 f/f TNFa 1

value: small intestinal organoids

value: Day 3, TNFa stimulation for 2hr


title: Basal + ACSL3 siRNA 2


title: Basal + ACSL3 siRNA 1


title: 292CON_re-used

description:
sample_33
GSM3954334


title: 22CON.1_re-used

description:
sample_27
GSM3954331


title: 5: Atg16L1 dIEC 1


title: TUBE FORMATION 3


title: 27CON_re-used

description:
sample_26
GSM3954330


title: 3: Atg16L1 f/f 3


title: 135CON.2_re-used

description:
sample_24
GSM3954329


title: TUBE FORMATION 1


title: TNF-alpha + control siRNA 3

value: TNF-alpha + control siRNA


title: TNF-alpha + control siRNA 2


title: 2: Atg16L1 f/f 2

value: Day 3, no stimulation


title: 1: Atg16L1 f/f 1


title: 22CON.2_re-used

description:
sample_28
GSM3954332


title: 135CON.1_re-used

description:
sample_23
GSM3954328


title: 51CON_re-used

description:
sample_21
GSM3954327


title: TUBE FORMATION 2


title: TNF-alpha + control siRNA 1

value: Human coronary artery endothelial cells


title: 15CON_re-used

description:
sample_20
GSM3954326


title: 4: Atg16L1 f/f 4


title: Basal + control siRNA 3

value: Female

value: Basal + control siRNA


title: 300CON.2_re-used

description:
sample_8
GSM3954325


title: Basal + control siRNA 2

value: 40 yrs


title: TUBE FORMATION 4


title: CONTROL 4

value: control


title: CONTROL 5


title: 300CON.1_re-used

description:
sample_7
GSM3954324

value: Human iPSC derieved cerebral organoids


title: Basal + control siRNA 1


title: CONTROL 3


title: CONTROL 6


title: PP10

city: Qingdao

first: Xiaofeng

last: Sun

address: 700 changcheng road

institute: Qingdao Agricultural University

description: single-end sequence reads

data_processing:
The expression level of miRNAs were quantitatively analyzed using MiRDeep2 software.
R package DESeq2 was used to normalize the expression level of miRNAs. The miRNAs with expression level of |log2FoldChange|>2 and FDR <0.05 were regard as differentially expressed miRNAs.
Genome_build: mm10
Supplementary_files_format_and_content: The miRNA expression matrix is stored as tab-delimited text files after normalization.

extract_protocol:
The isolated ovaries were homogenized in TRIZOL to extract total RNA.
miRNA-seq were performed using HiSeq 2500 sequencer at Novogene Bioinformatics Technology Co., Ltd

tag: strain

value: Ovary

value: 10μM DEHP treatment


title: PP100

description: single-end sequence reads

tag: treatment

value: 100μM DEHP treatment


title: Fetal_HeliosKO_TGFbiTreg_5

status: Public on Nov 22 2019

city: San Francisco

first: Melissa

last: Ng

state: California

address: 35 Medical Centre Way, Regeneration Medicine Building 903B

institute: University of California, San Francisco

description:
Sequencing batch 2
TMM_normalizedreads_iTregHeliosKOvsWT.txt

data_processing:
Fastq files were mapped to hg19 with Bowtie 2
Read counts per gene was obtained using RSEM
TMM normalization and differential expression analysis performed using EdgeR package for Bioconductor
Separate comparisons were performed for adult and fetal iTreg cells, and fetal HeliosKO and HeliosWT iTreg cells using generalized linear models
TMM read counts for HeliosKO versus HeliosWT comparisons are normalized for paired samples and batch effects due to two sequencing runs carried out, and are supplied as log2 read counts.
Genome_build: hg19
Supplementary_files_format_and_content: Generalized linear model output with fold change and FDR in text files for both comparisons. TMM normalized read counts for both comparisons in txt files.

source_name: Fetal spleenocytes

growth_protocol: Treg differentiation - Cells were stimulated with anti-CD3/CD28/CD2 tetratmers (Stemcell) in culture media supplemented with with 10ng/mL IL-2 (Peprotech) in the presence of absence of 50ng/mL TGFb (Peprotech)

extract_protocol:
Cells were harvested on Day 6 of culture, and total RNA was extracted from 25,000 cells using the Nucleospin XS RNA kit (Machery Nagel)
Libraries were constructed using a standard Illumina protocol following manufactorer instructions using the NEBNext® Ultra™ II Directional RNA Library Prep Kit

treatment_protocol: For fetal iTreg cells,CRISPR-Cas9 editing via nucleofection of Cas9 complex with the Helios gRNA1 (HeliosKO) or non-targeting guide (HeliosWT) was carried out prior to Treg differentiation

tag: donorid

tag: genotype

value: Helios Knockout

value: 21.3 weeks

tag: Sex


title: Fetal_HeliosKO_TGFbiTreg_7

value: 23.6 weeks

value: Male


title: Fetal_HeliosKO_TGFbiTreg_6

value: 23 weeks

value: Not determined


title: Fetal_HeliosWT_TGFbiTreg_6

value: Wildtype


title: Fetal_HeliosKO_IL2iTreg_6


title: Fetal_HeliosWT_TGFbiTreg_5


title: CONTROL 1

value: PRIMARY CELLS


title: Fetal_HeliosWT_IL2iTreg_5


title: Fetal_HeliosKO_IL2iTreg_4

description:
Sequencing batch 1
TMM_normalizedreads_iTregHeliosKOvsWT.txt

value: 22.2 weeks


title: Fetal_HeliosKO_TGFbiTreg_1

value: 21.1 weeks


title: Fetal_HeliosKO_IL2iTreg_7


title: PP0

description: single-end sequence reads

value: 0μM DEHP treatment


title: Fetal_HeliosKO_IL2iTreg_3


title: Fetal_HeliosKO_IL2iTreg_5


title: Fetal_HeliosWT_TGFbiTreg_7


title: Fetal_HeliosWT_IL2iTreg_7


title: Fetal_HeliosKO_IL2iTreg_1


title: Fetal_HeliosKO_TGFbiTreg_3


title: Fetal_HeliosKO_TGFbiTreg_4

value: Female


title: Fetal_HeliosWT_TGFbiTreg_3

description:
Sequencing batch 1
TMM_normalizedreads_iTregFetalvsAdult.txt, TMM_normalizedreads_iTregHeliosKOvsWT.txt


title: Fetal_HeliosWT_TGFbiTreg_2

description:
Sequencing batch 1
TMM_normalizedreads_iTregFetalvsAdult.txt

value: 20.5 weeks


title: Adult_TGFbiTreg_4

source_name: Human PBMCs

value: 48 years


title: Adult_TGFbiTreg_3

value: 62 years


title: Fetal_HeliosWT_IL2iTreg_3


title: Fetal_HeliosWT_TGFbiTreg_1


title: Adult_TGFbiTreg_1

value: Unknown


title: Fetal_HeliosWT_IL2iTreg_1


title: Fetal_HeliosWT_IL2iTreg_2


title: Adult_IL2iTreg_4


title: Fetal_HeliosWT_IL2iTreg_6


title: Adult_IL2iTreg_1

value: Undetermined


title: Adult_IL2iTreg_2


title: Adult_IL2iTreg_3


title: Input_FNrep2

library_source: genomic

data_processing:
Fastq files were mapped to the genome using Bowtie 2 with the following parameters: -p 10 -q -D 15 -R 10 -L 22 -i S,1,1.15
Mapped reads were filtered to keep uniquely mapping, non-duplicated reads using Samtools. Reads with q>30 were kept.
MACS2 was used for peak calling for ChIPseq dataset using the following settings: callpeak -t ${K27ac_SAMPLE} -c ${INPUT} -f BAM -g hs -q 0.01
The ROSE algorithm was used to define superenhancers. Briefly, each peak file for each ChIPseq replicate was converted into GFF format and peaks within 2kb of the TSS were removed. Superenhancer calling was performed with the following settings: -g hg19 -i ${GFF} -r ${K27acBAM}  -c ${INPUTBAM}  -s 12500 -o ${OUTPUT}
Generation of read count tables across a masterlist of all superenhancers/transcriptional enhancers for DESeq2 analysis. Enhancers across all replicates were merged using bedops -merge to create a masterlist of SEs and Tes shared across all cell types and cell origin. Bedtools -multicov was utilized to map reads from ATACseq and ChIPseq bam files onto enhancer regions.
Bigwig files for ATACseq were generated by first calculating tag densities as the number of tags that map to within 75 bp of each 20bp genomic bin. Tag insertion positions were calculated as +4bp from the upstream end of + strand tags and -5 bp from - strand tags. Blacklist regions were also removed using known regions from the ENCODE consortium. Regions with tag density greater than 40 were identified as accessible regions.
Bigwig files for ChIPseq were generated by first calculating tag density. The midpoint of each fragment size for each sample replicate was calculated and tags were mapped to within 75 bp of each 20bp genomic bin for both input and immunoprecipitated samples. Blacklist regions were also removed using known regions from the ENCODE consortium. Tag counts were normalized to library size, and input counts were subtracted before conversion into the bigwig format
Genome_build: hg19
Supplementary_files_format_and_content: BED file of all merged superenhancers/transcriptional enhancers. Bigwig files for each individual biological replicate for ATACseq and H3K27c ChIPseq

extract_protocol:
Cells were sorted by FACS, and DNA was extracted from lysed cells following conventional ATACseq and ChIPseq protocols
ATACseq libraries were constructed using the standard Illumina Nextera protocol. H3K27ac ChIPseq libraries were constructed using a standard Illumina protocol using Truseq adapters.

value: Fetal spleenocytes

value: 23.0 weeks

tag: sequencing adapter

value: CGATGT

value: fetal naive T cells


title: Input_FNrep3

value: ACAGTG


title: Input_ATrep3

value: Human PBMCs

value: 26 years

value: Male

value: CAGATC

value: adult CD4+CD25hiCD127lo regulatory T


title: Adult_TGFbiTreg_2

value: Wildtype


title: Input_ATrep1

value: 50 years

value: Female


title: Input_ANrep3

value: GCCAAT

value: adult CD4+CD25-CD45RA+CD27+ naive T cells


title: CONTROL 2

value: PRIMARY CELLS

value: control


title: Input_FNrep1

value: Fetal spleenocytes


title: H3K27ac_FNrep3

value: 21.1 weeks


title: Fetal_HeliosWT_IL2iTreg_4

value: 22.2 weeks


title: Input_ATrep2

value: 70 years

value: TGACCA


title: H3K27ac_FNrep2

value: 23.0 weeks

value: CGATGT

value: fetal naive T cells


title: Fetal_HeliosWT_TGFbiTreg_4


title: Input_ANrep1

value: Human PBMCs


title: Input_ANrep2

value: Male

value: TTAGGC


title: H3K27ac_FNrep1

value: ACAGTG


title: H3K27ac_ATrep3

value: 26 years

value: CAGATC

value: adult CD4+CD25hiCD127lo regulatory T


title: H3K27ac_ANrep2

value: adult CD4+CD25-CD45RA+CD27+ naive T cells


title: H3K27ac_ANrep3

value: GCCAAT


title: hAD-MSC_C0.02_3Days

city: Pocheon-si

first: Jae Ho

last: Lee

state: Gyeonggi-do

address: 120, Haeryong-ro

department: Department of biomedical Science

country: South Korea

institute: CHA University

description: mRNA-seq

data_processing:
FastQC was used to evaluate quality of sequenced reads (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Contaminated adaptor portions of sequenced reads were trimmed using the Trim Galore program (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Sequenced reads were mapped to reference human genome (hg19 assembly) using STAR aligner (2.5.2b, Dobin et al., 2013 Bioinformatics) with default parameters.
Cufflinks version 2.2.1 (Trapnell et al., 2012 Nat Protoc) was used to estimate the abundance (FPKM) of transcripts.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: human adipose-derived mesenchymal stem cells (hAD-MSCs)

growth_protocol: The hAD-MSCs were purchased from company (HUXMD-01001, Cyagen Biosciences Inc. CA, US) and cultured with MSC media (HUXMD-90011, Cyagen Biosciences Inc. CA US) and 1% penicillin/streptomycin (10378016; Invitrogen life technique, NY, USA) maintained at a temperature of 37 °C in a humidified atmosphere containing 5% CO2. The hAD-MSCs were harvested for subculture every 3 days. We have post trypsinization, washing and re-suspending at 1 x 10-5cells ml concentration in normal growth medium.

extract_protocol:
After electrical stimulated hAD-MSCs were harvested by trypsinization and washed by PBS, the cells were stored at -80 ºC for mRNA purification. All samples were isolated using the mRNA purification kit (RNeasy Mini Kit; 74104, Qiagen US).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The EBFC electrodes were prepared using an enzyme loading solution. The loading solutions for enzyme electrodes composed of enzyme, redox mediator, and cross-linker. The anodic catalyst comprised a cross-linked adduct of GOx (Amano Enzyme Inc. Japan: 0.05, 0.02, and 0.01 mg/mL), PVI-[Os(dmo-bpy)2Cl]+/2+ (1 mg/mL), and PEGDGE (poly(ethylene glycol) diglycidyl ether; 5.0 mg/mL) in the volume ratio of 4: 4: 1.

value: Human Adipose-Derived Mesenchymal Stem Cells

tag: treatment duration

value: 3 days


title: H3K27ac_ATrep2


title: H3K27ac_ANrep1

value: 50 years

value: Female


title: H3K27ac_ATrep1


title: hAD-MSC_C0.05_3Days

description: mRNA-seq


title: hAD-MSC_C0.01_3Days

description: mRNA-seq


title: K562-WT (wild-type) - RNAseq_ Repeated

city: Hyderabad

first: Ramakrishna

last: Kancha

address: Osmania University Main Campus

institute: Osmania University

description: Imatinib-sensitive

data_processing:
The decontaminated data set was mapped to the human genome [hg19] using hisat 2-2.1.0.
Reads mapping to genes [hg19 gene list GTF] were counted using featurecount module of subreads package.
The read counts were normalized using DESeq2-3.5 to identify the differentially expressed  genes.
Significantly affected differentially expressed genes were selected based on 1.5x fold change, and
then an adjusted P-value of < 0.05.
Genome_build: hg19

source_name: Human leukemia cell line

growth_protocol: Cells grown in RPMI1640 supplemented with 10%FBS and antibiotics

extract_protocol:
Total RNA was isolated and cDNA libraries were constructed from wild type and imatinib-resistant cell lines.
The transcriptome libraries were constructed and sequenced on Illumina HiSeq.

treatment_protocol: Cell lines K562-IR1 and K562-IR2 are grown in continuous presence of imatinib

tag: cell line

value: K562 Imatinib-sensitive

value: Human leukemia cell line


title: K562-IR1 (imatinib-resistant 1) - RNAseq

description: Imatinib-resistant

source_name: Human leukemia cell line derived

value: K562 Imatinib-resistant

value: Human leukemia cell line derived


title: K562-IR1 (imatinib-resistant 1) - RNAseq_Repeated

description: Imatinib-resistant


title: K562-IR2 (imatinib-resistant 2) - RNAseq

description: Imatinib-resistant


title: K562-WT (wild-type) - RNAseq

description: Imatinib-sensitive


title: K562-IR2 (imatinib-resistant 2) - RNAseq_Repated

description: Imatinib-resistant


title: hAD-MSC_Con

description: mRNA-seq

value: control


title: LDG_SLE_06_imm [ATAC-seq]

city: Bethesda

first: Hong-wei

state: MD

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

description:
A22
Exp ID: 170201_0368_s28

data_processing:
Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. PE reads of 50 bases were mapped to the hg19 using Bowtie 1.1.1.
Peak calling: Redundant reads were removed using Fastquniq. Uniquely mapped reads from fragments less than 175 bp were used to call peaks with MACS 2.1.1 using a p-value threshold of 1 x 10-5.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig files

source_name: Human whole blood

extract_protocol:
Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. LDGs were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies.
ATAC-seq was performed according to a published protocol (Buenrostro et al., 2013) with minor modification. 100,000 cells performed in quadruplicate for each sample were treated with the Tn5 transposase (Illumina) for 30 min at 37°C and PCR-purified (Qiagen) to generate library fragments.
ATAC seq data were generated on Illumina HiSeq 2500 instruments according to the manufacturer's instructions.

tag: diagnosis

value: Lupus

value: LDG


title: LDG_SLE_04_mat [ATAC-seq]

description:
A20
Exp ID: 170201_0368_s04


title: LDG_SLE_08_mat [ATAC-seq]

description:
A24
Exp ID: 170201_0368_s52


title: LDG_SLE_07_imm [ATAC-seq]

description:
A23
Exp ID: 170201_0368_s40


title: LDG_SLE_05_mat [ATAC-seq]

description:
A21
Exp ID: 170201_0368_s16


title: LDG_SLE_02_imm [ATAC-seq]

description:
A18
Exp ID: 151013_0265_s13


title: LDG_SLE_03_mat [ATAC-seq]

description:
A19
Exp ID: 151013_0265_s21


title: LDG_SLE_01_mat [ATAC-seq]

description:
A17
Exp ID: 151013_0265_s05


title: NDN_SLE_05 [ATAC-seq]

description:
A13
Exp ID: 170201_0368_s12

value: NDN


title: NDN_SLE_08 [ATAC-seq]

description:
A16
Exp ID: 170201_0368_s48


title: NDN_SLE_01 [ATAC-seq]

description:
A09
Exp ID: 151013_0265_s01


title: NDN_SLE_07 [ATAC-seq]

description:
A15
Exp ID: 170201_0368_s36


title: NDN_ctrl_03 [ATAC-seq]

description:
A03
Exp ID: 151013_0265_s33

value: Healthy (control)


title: NDN_ctrl_01 [ATAC-seq]

description:
A01
Exp ID: 151013_0265_s25


title: NDN_SLE_03 [ATAC-seq]

description:
A11
Exp ID: 151013_0265_s17


title: NDN_SLE_04 [ATAC-seq]

description:
A12
Exp ID: 170201_0368_s01


title: NDN_SLE_02 [ATAC-seq]

description:
A10
Exp ID: 151013_0265_s09


title: ERa ChIP-seq_E2 treatment_WT_Rep1

city: Bangalore

first: Bharath

last: Saravanan

state: Karnataka

address: Bellary Road

department: Genetics and Development

institute: National centre for Biological Sciences

description: ERa

data_processing:
Basecalls performed using standard illumina pipeline
ChIP-seq reads were aligned to the genome assembly using Bowtie 2 version 2.3.0 with default configurations
HOMER was used to build Tag directories using -unique -tbp 1
peaks were called using HOMER findPeaks  with the following setting: -style factor -L 3 -o auto -o auto.
5C Reads were mapped to an artificial genome of all possible combinations of forward and reverse primers using Bowtie2.
The uniquely mapped 5C reads were then used to build a matrix of interactions between all the reverse and forward primers. The intra-chromosome 21 primers interactions were then normalized to their interactions with chr16 gene dessert for each interaction combination.
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files were generated using HOMER makeUCSCfile

source_name: MCF7 cells

growth_protocol: MCF7 cells were stripped for 3 days (sample 1-6) in charcoal stripped media. Cells were stripped for 7 days in case of sample 7

extract_protocol:
ChIP-seq, ERa bound regions were pull down using antibody. 5C, chromatin interactions were detected by 5C
Libraries were prepared using standard ChIP-seq library protocol
For 5C, Set of forward and reverse oligos with T7 and T3 adaptors were anneled to 3C libraies. The ligated oligos were amplified and sequenced on illumina Hiseq 2500 platform

treatment_protocol: MCF7 cells were stripped for 3 days in charcoal stripped media and treated with either ICI (24h) or E2 (1hr) followed by ChIP-seq or 5C

tag: treatments

value: Estradiol 1 hr

tag: antibody

value: MCF7 cells


title: NDN_ctrl_08 [ATAC-seq]

description:
A08
Exp ID: 170201_0368_s56

tag: cell type


title: NDN_ctrl_07 [ATAC-seq]

description:
A07
Exp ID: 170201_0368_s44


title: 5C_E2_1hr_Rep2

description: targated chromatin interactions

data_processing:
Library strategy: 5C
Basecalls performed using standard illumina pipeline
ChIP-seq reads were aligned to the genome assembly using Bowtie 2 version 2.3.0 with default configurations
HOMER was used to build Tag directories using -unique -tbp 1
peaks were called using HOMER findPeaks  with the following setting: -style factor -L 3 -o auto -o auto.
5C Reads were mapped to an artificial genome of all possible combinations of forward and reverse primers using Bowtie2.
The uniquely mapped 5C reads were then used to build a matrix of interactions between all the reverse and forward primers. The intra-chromosome 21 primers interactions were then normalized to their interactions with chr16 gene dessert for each interaction combination.
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files were generated using HOMER makeUCSCfile


title: NDN_ctrl_06 [ATAC-seq]

description:
A06
Exp ID: 170201_0368_s32


title: NDN_ctrl_04 [ATAC-seq]

description:
A04
Exp ID: 170201_0368_s08


title: NDN_ctrl_02 [ATAC-seq]

description:
A02
Exp ID: 151013_0265_s29


title: 5C_E2_1hr_Rep1

description: targated chromatin interactions


title: 5C_ICI_Rep2

description: targated chromatin interactions


title: ERa ChIP-seq_7days stripping

description: ERa

value: 7 days stripped cells


title: NDN_ctrl_05 [ATAC-seq]

description:
A05
Exp ID: 170201_0368_s20


title: 5C_ICI_Rep1

description: targated chromatin interactions


title: ERa ChIP-seq_E2 treatment_DTFF1 persistent site_Rep1

description: ERa

source_name: MCF7 cells with PS deletion

value: MCF7 cells with PS deletion


title: E8_580mins

city: Gainesville

first: Rhonda

last: Bacher

state: FL

address: 2004 Mowry Rd.

institute: University of Florida

description:
hg19genes.no_mt.ec.tab
hg19genes.no_mt.tpm.rescale.tab

data_processing:
Illumina bclToFastq-1.8.4 used for basecalling the HiSeq2500 Files, and bcl2fastq2-v2.17.1.14 for basecalling the HiSeq3000 Files.
Reads were filtered and trimmed for adapters and quality. Expression estimates were calculated using RSEM v1.2.3 with alignments by bowtie v0.12.9 to mm10 (mouse) & hg19 (human) transcriptomes.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19 & mm10
Supplementary_files_format_and_content: Tab-delimited text files include expected count (EC) values and TPM-normalized counts for each sample.

growth_protocol: H1 human ES cells were routinely maintained as undifferentiated in E8 medium. Mouse Epiblast stem cells (mEpiSCs) were maintained on MEFs in TSS maintenance medium (DMEM/F12 (Thermo Fisher Scientific, USA), 20% knockout serum replacement (Thermo Fisher Scientific, USA), 0.18 mM B-mercaptoethanol (Sigma, USA), 1 X non-essential amino acids (Thermo Fisher Scientific, USA), 2 mM L-glutamine (Sigma, USA), 7.5 ng/mL activin A (R&D Systems, USA), and 5 ng/mL bFGF (R&D Systems, USA))

extract_protocol:
Cells grown in 6-well or 12-well plates were washed with PBS and lysed with RLT Plus lysis buffer (Qiagen), stored in -20C for 24 hours and then -80C until later processing. Total RNA was purified from the RLT Plus lysates using the RNeasy Plus Mini Kits (Qiagen) according to manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard the LM-seq protocol.

treatment_protocol: Neural differentiaion was induced with neural induction medium (DF3S (Thermo Fisher Scientific, USA) supplemented with 1 X N2 supplement (Thermo Fisher Scientific, USA), 1 X B27 supplement (Thermo Fisher Scientific, USA), and 100 ng/µL of mNoggin (R&D Systems, USA)). Control medium consisted of E8 pluripotency maintenance medium for H1 cells.

value: hES cells

value: E8 medium

tag: time

value: 580 min


title: E8_600mins

value: 600 min


title: E8_590mins

value: 590 min


title: E8_560mins

value: 560 min


title: E8_550mins

value: 550 min


title: E8_520mins

value: 520 min


title: E8_540mins

value: 540 min


title: E8_500mins

value: 500 min


title: E8_510mins

value: 510 min


title: E8_490mins

value: 490 min


title: ERa ChIP-seq_E2 treatment_DTFF1 persistent site_Rep2

description: ERa


title: E8_460mins

value: 460 min


title: E8_480mins

value: 480 min


title: E8_430mins

value: 430 min


title: E8_420mins

value: 420 min


title: E8_410mins

value: 410 min


title: E8_400mins

value: hES cells

value: 400 min


title: E8_530mins

value: E8 medium

value: 530 min


title: E8_570mins

value: 570 min


title: E8_450mins

value: 450 min


title: E8_390mins

value: 390 min


title: SED2_T0

city: Granada

first: Jorge

last: Molina

address: Campus de la Cartuja S/N

institute: University of Granada

description:
Sedentary
SAMPLE 2

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software Expression Suite for QuantStudio 12K Flex Real-Time PCR System (Applied Biosystems, Thermo Fisher Scientific, Carlsbad, CA, USA). http://sabiosciences.com/pcrarraydataanalysis.php
A total of 52 genes were included in the analysis in order to determine the stability value (M) and the coefficient of variation of the normalized reference gene expression levels using qBasePLUS software (Biogazelle, Gent, Belgium).
The selected housekeeping genes were: ATP5B (ATP synthase H+ transporting, mitochondrial F1 complex, beta polypeptide; NC_000076.6; gene expression assay Hs00969569_m1, Applied Biosystems); LUC7L2 (LUC7 like 2, pre-RNA splicing factor; NC_000007.14; gene expression assay Hs00255388_m1, Applied Biosystems); ARF1 (ADP-ribosylation factor 1; NC_000001.11; gene expression assay Hs00734523_m1, Applied Biosystems); and PAPOLA (Poly(A) polymerase alpha; NC_000014.9; gene expression assay Hs00413685_m1, Applied Biosystems). The mean of the housekeeping genes to use as the value for normalization.
Target gene signals normalized to housekeeping genes, where deltaCt = (Ct_Target − Ct_HKG)]

source_name: Total blood samples

extract_protocol: Total RNA was extracted with PAXgene blood RNA tube (Becton Dickinson, Germany) by DNase I treatment. The RNA yield was estimated by measuring absorbance at 260 nm in a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific). RNA purity was calculated from the ratio of absorbance at 260 nm and 280 nm. The OD 260/280 ratio was between 1.9 and 2.2 for all samples. RNA integrity was assessed using the Eukaryote Total RNA Nano assay on an Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: subject id

value: Total blood

tag: activation agent

value: Control group

value: T0 (baseline)


title: E8_470mins

value: 470 min


title: E8_370mins

value: 370 min


title: E8_360mins

value: 360 min


title: E8_320mins

value: 320 min


title: E8_340mins

value: 340 min


title: E8_350mins

value: 350 min


title: E8_300mins

value: 300 min


title: E8_310mins

value: hES cells

value: 310 min


title: NDN_SLE_06 [ATAC-seq]

description:
A14
Exp ID: 170201_0368_s24

value: Lupus

value: NDN


title: E8_290mins

value: E8 medium

value: 290 min


title: E8_280mins

value: 280 min


title: E8_260mins

value: 260 min


title: E8_270mins

value: 270 min


title: E8_440mins

value: 440 min


title: E8_240mins

value: 240 min


title: E8_250mins

value: 250 min


title: E8_230mins

value: 230 min


title: E8_190mins

value: 190 min


title: E8_220mins

value: 220 min


title: E8_200mins

value: 200 min


title: E8_380mins

value: 380 min


title: E8_180mins

value: hES cells

value: 180 min


title: E8_170mins

value: 170 min


title: SED11_T0

description:
Sedentary
SAMPLE 11

tag: tissue

value: Total blood

value: Control group

value: T0 (baseline)


title: E8_210mins

value: E8 medium

value: 210 min


title: E8_160mins

value: 160 min


title: E8_110mins

value: 110 min


title: E8_330mins

value: 330 min


title: E8_140mins

value: 140 min


title: E8_150mins

value: 150 min


title: E8_90mins

value: 90 min


title: E8_100mins

value: 100 min


title: E8_80mins

value: 80 min


title: E8_70mins

value: 70 min


title: E8_60mins

value: hES cells

value: 60 min


title: E8_130mins

value: 130 min


title: E8_50mins

value: 50 min


title: E8_40mins

value: 40 min


title: E8_30mins

value: 30 min


title: E8_20min

value: E8 medium

value: 20 min


title: E8_0_045220_0039683

value: E8 before neural induction

value: 0 min


title: NBplusNog_600min_038973_0039847

value: Neural induction medium

value: 600 min


title: NBplusNog_600min_038973_0023695


title: NBplusNog_590min_038972_0023694

value: 590 min


title: NBplusNog_570min_038970_0039844

value: 570 min


title: NBplusNog_570min_038970_0023692


title: NBplusNog_580min_038971_0039845

value: 580 min


title: NBplusNog_560min_038969_0023691

value: 560 min


title: NBplusNog_560min_038969_0039843


title: NBplusNog_550min_038968_0039842

value: 550 min


title: NBplusNog_550min_038968_0023690

value: hES cells


title: NBplusNog_540min_038967_0039841

value: 540 min


title: NBplusNog_540min_038967_0023689


title: NBplusNog_590min_038972_0039846


title: NBplusNog_530min_038966_0023688

value: 530 min


title: E8_120mins

value: 120 min


title: NBplusNog_520min_038965_0039839

value: 520 min


title: NBplusNog_510min_038964_0039838

value: 510 min


title: NBplusNog_510min_038964_0023686


title: NBplusNog_520min_038965_0023687


title: NBplusNog_500min_038963_0023685

value: 500 min


title: NBplusNog_500min_038963_0039837


title: E8_10min

value: E8 medium

value: 10 min


title: NBplusNog_490min_038962_0039836

value: 490 min


title: NBplusNog_490min_038962_0023684

value: Neural induction medium


title: NBplusNog_580min_038971_0023693


title: NBplusNog_480min_038961_0023683

value: 480 min


title: NBplusNog_460min_038959_0039833

value: 460 min


title: NBplusNog_470min_038960_0023327

value: 470 min


title: NBplusNog_470min_038960_0039834


title: NBplusNog_460min_038959_0023326


title: NBplusNog_450min

value: 450 min


title: NBplusNog_440min_038957_0039832

value: 440 min


title: NBplusNog_430min_038956_0039831

value: 430 min


title: NBplusNog_440min_038957_0023325

value: hES cells


title: NBplusNog_530min_038966_0039840


title: NBplusNog_420min_038955_0023323

value: 420 min


title: NBplusNog_410min_038954_0023322

value: 410 min


title: NBplusNog_400min_038953_0039828

value: 400 min


title: NBplusNog_390min_038952_0039827

value: 390 min


title: NBplusNog_390min_038952_0023320


title: NBplusNog_400min_038953_0023321


title: NBplusNog_370min_038950_0023318

value: 370 min


title: NBplusNog_380min_038951_0039826

value: 380 min


title: NBplusNog_370min_038950_0039825


title: NBplusNog_480min_038961_0039835


title: NBplusNog_360min_038949_0023317

value: 360 min


title: NBplusNog_360min_038949_0039824


title: NBplusNog_380min_038951_0023319


title: NBplusNog_340min_038947_0039822

value: 340 min


title: NBplusNog_350min_038948_0023316

value: 350 min


title: NBplusNog_350min_038948_0039823

value: Neural induction medium


title: NBplusNog_340min_038947_0023315


title: NBplusNog_330min_038946_0023314

value: 330 min


title: NBplusNog_420min_038955_0039830


title: NBplusNog_330min_038946_0039821


title: NBplusNog_320min_038945_0039820

value: 320 min


title: NBplusNog_310min_038944_0023312

value: 310 min


title: NBplusNog_300min_038943_0039818

value: 300 min


title: NBplusNog_310min_038944_0039819


title: NBplusNog_320min_038945_0023313


title: NBplusNog_410min_038954_0039829


title: NBplusNog_300min_038943_0023311


title: NBplusNog_290min_038942_0039817

value: 290 min


title: NBplusNog_290min_038942_0023310


title: NBplusNog_280min_038941_0039816

value: 280 min


title: NBplusNog_270min_038940_0039815

value: hES cells

value: 270 min


title: NBplusNog_430min_038956_0023324

value: 430 min


title: NBplusNog_260min_038939_0039814

value: 260 min


title: NBplusNog_230min_038936_0039811

value: 230 min


title: NBplusNog_260min_038939_0023307


title: NBplusNog_250min_038938_0039813

value: 250 min


title: NBplusNog_230min_038936_0023304


title: NBplusNog_240min_038937_0023305

value: 240 min


title: NBplusNog_250min_038938_0023306


title: HN4: Uninfected Normal Liver tissue (Total RNA-Seq)

description:
Normal Liver Tissue from Gall Bladdar Carcinoma patients after histological verification
CLR2-HN4

value: Normal Liver Tissue

tag: etiology

value: Uninfected

tag: gender

value: Male


title: NBplusNog_220min_038935_0039810

tag: treatment

value: Neural induction medium

value: 220 min


title: NBplusNog_240min_038937_0039812


title: NBplusNog_210min_038934_0023302

value: 210 min


title: NBplusNog_210min_038934_0039809


title: NBplusNog_220min_038935_0023303


title: NBplusNog_200min_038933_0039808

value: 200 min


title: NBplusNog_190min_038932_0023300

value: 190 min


title: NBplusNog_200min_038933_0023301


title: NBplusNog_170min_038930_0039805

value: 170 min


title: NBplusNog_170min_038930_0023298


title: NBplusNog_280min_038941_0023309

value: 280 min


title: NBplusNog_190min_038932_0039807

value: hES cells


title: NBplusNog_160min_038929_0039804

value: 160 min


title: NBplusNog_180min_038931_0023299

value: 180 min


title: NBplusNog_150min_038928_0039803

value: 150 min


title: NBplusNog_180min_038931_0039806


title: NBplusNog_270min_038940_0023308

value: 270 min


title: NBplusNog_140min_038927_0023295

value: 140 min


title: NBplusNog_150min_038928_0023296


title: NBplusNog_130min_038926_0023294

value: 130 min


title: NBplusNog_140min_038927_0039802


title: NBplusNog_130min_038926_0039801


title: NBplusNog_110min_038924_0039799

value: 110 min


title: NBplusNog_110min_038924_0023292


title: NBplusNog_90min_038922_0039797

value: 90 min


title: NBplusNog_90min_038922_0023290


title: NBplusNog_80min_038921_0039796

value: 80 min


title: NBplusNog_100min_038923_0039798

value: Neural induction medium

value: 100 min


title: NBplusNog_80min_038921_0023289


title: NBplusNog_160min_038929_0023297


title: m_0

description:
mm10genes.no_mt.ec.tab
mm10genes.no_mt.tpm.rescale.tab

value: Mouse Epiblast stem cells

value: TSS prior to neural induction

value: 0 min


title: NBplusNog_50min_038918_0039793

value: 50 min


title: NBplusNog_50min_038918_0023286


title: NBplusNog_40min_038917_0023285

value: 40 min


title: NBplusNog_60min_038919_0023287

value: hES cells

value: 60 min


title: m_596_rep_2

value: 596 min


title: NBplusNog_40min_038917_0039792


title: NBplusNog_30min_038916_0039791

value: 30 min


title: m_600_rep_2

value: 600 min


title: NBplusNog_20min_038915_0039790

value: 20 min


title: NBplusNog_100min_038923_0023291


title: m_584_rep_2

value: 584 min


title: NBplusNog_120min_038925_0023293

value: 120 min


title: m_592_rep_2

value: 592 min


title: NBplusNog_120min_038925_0039800


title: m_580_rep_2

value: 580 min


title: NBplusNog_60min_038919_0039794

value: Neural induction medium


title: m_572

value: 572 min


title: m_576

value: Mouse Epiblast stem cells

value: 576 min


title: NBplusNog_70min_038920_0023288

value: 70 min


title: NBplusNog_70min_038920_0039795


title: NBplusNog_10min_038914_0039789

value: 10 min


title: E8_0_038911_0023279

value: E8 before neural induction

value: 0 min


title: E8_0_038911_0039788

value: hES cells


title: NBplusNog_30min_038916_0023284


title: NHL-7 - d89 - VDJ

city: Cape Town

first: Valentin

last: Voillet

state: Western Cape

address: First Floor Wembley Square, 3 McKenzie St, Gardens

country: South Africa

institute: cape town hvtn immunology laboratory

description: NHL-7 - d89 sample - VDJ expression

data_processing:
Library strategy: VDJ-seq
Alignment and quantification have been done following the Cell Ranger Software Suite (2.1.0). The Cell Ranger Single-Cell Software Suite (version 2.1.0) was used to perform sample demultiplexing, barcode processing and single-cell 5' gene counting (http://10xgenomics.com/). First, raw base BCL files were demultiplexed using the cellranger mkfastq pipeline into sample-specific FASTQ files. Second, these FASTQ files were processed with the cellranger count pipeline. Each sample was analyzed separately. The Cell Ranger pipeline uses the STAR alignment software (Dobin et al., 2013) to align cDNA reads to the GRCh38 human reference genome. Aligned reads were then filtered for valid cell barcodes and unique molecular identifiers (UMIs). Cell barcodes with 1-Hamming-distance from a list of known barcodes were considered. UMIs with sequencing quality score > 10% and not homopolymers were retained as valid UMIs. A UMI with 1-Hamming-distance from another UMI with more reads, for a same gene and a same cell was corrected to this UMI with more reads. cellranger aggr was then used to aggregate samples together. A correction for sequencing depth was performed during the aggregation.
Gene expression: I6 (sample index): 6bp - R1 (10x barcode, UMI): 26bp - R2 (insert): 98bp. VDJ expression: I1 (sample index): 6bp - R1 (10x Barcode, UMI, switch oligo, insert): 150bp - R2 (insert): 150bp
Genome_build: GRCh38 - 10x reference
bam files can be converted to fastq using bamtofastq (https://support.10xgenomics.com/docs/bamtofastq)
Supplementary_files_format_and_content: [raw.expMatrix.csv] csv-delimited table of the aggregated UMI count matrix
Supplementary_files_format_and_content: [*clonotypes.csv] csv-delimited tables of unpaired clonotypes (VDJ)

extract_protocol:
CD8+ CAR-T cells were loaded onto a microfluidic chip lane to generate single cells encapsulated in Gel Bead-in-Emulsions (GEM) according to manufacturer's instructions (10x Genomics).
A 5' gene expression library and an enriched V(D)J library were constructed for each sample according to manufacturer's instructions (10x Genomics). NB: Two samples (NHL-6-IP and NHL-7-IP) have been sequenced using the same chromium index - VDJ cell barcodes were used to differentiate those two samples.
A sequencing depth of 50,000 reads/cell was targeted for the 5' gene expression library and 5000 reads/cell for the V(D)J library as recommended by 10x Genomics.

tag: id in raw.expmatrix.csv

tag: patient id

tag: disease state

value: NHL

tag: time point

tag: time point - 2

value: Late


title: m_568

tag: cell line

value: 568 min


title: m_560

value: 560 min


title: m_564

value: 564 min


title: m_556

value: 556 min


title: NHL-7 - d28 - VDJ

description: NHL-7 - d28 sample - VDJ expression

value: Contraction


title: NBplusNog_20min_038915_0023283

value: 20 min


title: m_588_rep_2

value: Neural induction medium

value: 588 min


title: NHL-7 - d12 - VDJ

description: NHL-7 - d12 sample - VDJ expression

value: Early


title: NHL-7 - IP - VDJ

description: NHL-7 - IP sample - VDJ expression

value: IP


title: m_552

value: Mouse Epiblast stem cells

value: 552 min


title: m_548

value: 548 min


title: NHL-6 - d102 - VDJ

description: NHL-6 - d102 sample - VDJ expression


title: NBplusNog_10min_038914_0023282

value: 10 min


title: NHL-6 - d29 - VDJ

description: NHL-6 - d29 sample - VDJ expression


title: m_544

value: 544 min


title: m_540

value: 540 min


title: NHL-6 - IP - VDJ

description: NHL-6 - IP sample - VDJ expression

value: NHL


title: NHL-6 - d12 - VDJ

description: NHL-6 - d12 sample - VDJ expression


title: CLL-2 - d83 - VDJ

description: CLL-2 - d83 sample - VDJ expression

value: CLL

value: Late


title: m_536

value: 536 min


title: CLL-2 - d29 - VDJ

description: CLL-2 - d29 sample - VDJ expression


title: m_532

value: 532 min


title: m_528

value: 528 min


title: CLL-2 - d12 - VDJ

description: CLL-2 - d12 sample - VDJ expression


title: m_524

value: 524 min


title: m_516

value: Neural induction medium

value: 516 min


title: CLL-1 - d112 - VDJ

description: CLL-1 - d112 sample - VDJ expression


title: CLL-2 - IP - VDJ

description: CLL-2 - IP sample - VDJ expression


title: m_520

value: 520 min


title: m_500

value: 500 min


title: m_504

value: Mouse Epiblast stem cells

value: 504 min


title: m_496

value: 496 min


title: CLL-1 - d21 - VDJ

description: CLL-1 - d21 sample - VDJ expression

value: Early


title: CLL-1 - IP - VDJ

description: CLL-1 - IP sample - VDJ expression

value: IP


title: NHL-7 - d89 - GE

description:
NHL-7 - d89 sample - Gene expression
raw.expMatrix.csv

data_processing:
Alignment and quantification have been done following the Cell Ranger Software Suite (2.1.0). The Cell Ranger Single-Cell Software Suite (version 2.1.0) was used to perform sample demultiplexing, barcode processing and single-cell 5' gene counting (http://10xgenomics.com/). First, raw base BCL files were demultiplexed using the cellranger mkfastq pipeline into sample-specific FASTQ files. Second, these FASTQ files were processed with the cellranger count pipeline. Each sample was analyzed separately. The Cell Ranger pipeline uses the STAR alignment software (Dobin et al., 2013) to align cDNA reads to the GRCh38 human reference genome. Aligned reads were then filtered for valid cell barcodes and unique molecular identifiers (UMIs). Cell barcodes with 1-Hamming-distance from a list of known barcodes were considered. UMIs with sequencing quality score > 10% and not homopolymers were retained as valid UMIs. A UMI with 1-Hamming-distance from another UMI with more reads, for a same gene and a same cell was corrected to this UMI with more reads. cellranger aggr was then used to aggregate samples together. A correction for sequencing depth was performed during the aggregation.
Gene expression: I6 (sample index): 6bp - R1 (10x barcode, UMI): 26bp - R2 (insert): 98bp. VDJ expression: I1 (sample index): 6bp - R1 (10x Barcode, UMI, switch oligo, insert): 150bp - R2 (insert): 150bp
Genome_build: GRCh38 - 10x reference
bam files can be converted to fastq using bamtofastq (https://support.10xgenomics.com/docs/bamtofastq)
Supplementary_files_format_and_content: [raw.expMatrix.csv] csv-delimited table of the aggregated UMI count matrix
Supplementary_files_format_and_content: [*clonotypes.csv] csv-delimited tables of unpaired clonotypes (VDJ)


title: NHL-7 - d28 - GE

description:
NHL-7 - d28 sample - Gene expression
raw.expMatrix.csv

value: Contraction


title: NHL-7 - IP - GE

description:
NHL-7 - IP sample - Gene expression
raw.expMatrix.csv

value: NHL


title: m_488

value: 488 min


title: NHL-6 - d102 - GE

description:
NHL-6 - d102 sample - Gene expression
raw.expMatrix.csv

value: Late


title: m_480

value: 480 min


title: m_476

value: 476 min


title: m_484

value: 484 min


title: CLL-1 - d38 - VDJ

description: CLL-1 - d38 sample - VDJ expression

value: CLL


title: NHL-6 - d12 - GE

description:
NHL-6 - d12 sample - Gene expression
raw.expMatrix.csv


title: m_472

value: Neural induction medium

value: 472 min


title: NHL-6 - IP - GE

description:
NHL-6 - IP sample - Gene expression
raw.expMatrix.csv


title: m_460

value: 460 min


title: m_456

value: 456 min


title: CLL-2 - d83 - GE

description:
CLL-2 - d83 sample - Gene expression
raw.expMatrix.csv


title: NHL-6 - d29 - GE

description:
NHL-6 - d29 sample - Gene expression
raw.expMatrix.csv


title: m_508

value: Mouse Epiblast stem cells

value: 508 min


title: CLL-2 - d12 - GE

description:
CLL-2 - d12 sample - Gene expression
raw.expMatrix.csv


title: CLL-2 - d29 - GE

description:
CLL-2 - d29 sample - Gene expression
raw.expMatrix.csv


title: CLL-2 - IP - GE

description:
CLL-2 - IP sample - Gene expression
raw.expMatrix.csv


title: m_444

value: 444 min


title: m_448

value: 448 min


title: NHL-7 - d12 - GE

description:
NHL-7 - d12 sample - Gene expression
raw.expMatrix.csv

value: Early


title: m_440

value: 440 min


title: CLL-1 - d112 - GE

description:
CLL-1 - d112 sample - Gene expression
raw.expMatrix.csv


title: m_436

value: 436 min


title: m_432

value: 432 min


title: CLL-1 - d21 - GE

description:
CLL-1 - d21 sample - Gene expression
raw.expMatrix.csv


title: m_420

value: 420 min


title: ATAC_FNrep4

value: Fetal spleenocytes

tag: age

value: 23.0 weeks

tag: Sex

value: Not collected

tag: sequencing adapter

value: ACCACTGT

value: fetal naive T cells


title: m_468

tag: cell type

value: Neural induction medium

value: 468 min


title: ATAC_FNrep3

value: GTCGTGAT


title: ATAC_FNrep2

value: 22.5 weeks

value: TAGGCATG


title: ATAC_FNrep1

value: GGACTCCT


title: m_416

value: Mouse Epiblast stem cells

tag: time

value: 416 min


title: m_412

value: 412 min


title: CLL-1 - d38 - GE

description:
CLL-1 - d38 sample - Gene expression
raw.expMatrix.csv

value: CLL

value: Contraction


title: m_404

value: 404 min


title: ATAC_ATrep2

value: Human PBMCs

value: TCCTGAGC

value: adult CD4+CD25hiCD127lo regulatory T


title: ATAC_ATrep4

value: Not collected

value: AAGAGGCA


title: ATAC_ATrep3

value: CGAGGCTG


title: m_408

value: Neural induction medium

value: 408 min


title: m_396

value: 396 min


title: m_428

value: 428 min


title: CLL-1 - IP - GE

description:
CLL-1 - IP sample - Gene expression
raw.expMatrix.csv

value: IP


title: m_400

description:
mm10genes.no_mt.ec.tab
mm10genes.no_mt.tpm.rescale.tab

value: Mouse Epiblast stem cells

value: 400 min


title: ATAC_ANrep4

value: CAGAGAGG

value: adult CD4+CD25-CD45RA+CD27+ naive T cells


title: m_392

value: 392 min


title: m_388

value: 388 min


title: ATAC_ANrep3

value: Human PBMCs

value: CTCTCTAC


title: ATAC_ATrep1

value: AGGCAGAA

value: adult CD4+CD25hiCD127lo regulatory T


title: m_384

value: 384 min


title: ATAC_ANrep2

value: Not collected

value: CGTACTAG


title: m_380

value: Neural induction medium

value: 380 min


title: m_376

value: 376 min


title: m_372

value: 372 min


title: ATAC_ANrep1

value: TAAGGCGA


title: m_368

value: Mouse Epiblast stem cells

value: 368 min


title: m_360

value: 360 min


title: m_364

value: 364 min


title: sscontrol_bm_sthsc_R3

city: Oxford

first: Stephen

last: Sansom

state: Oxfordshire

address: Roosevelt Drive

department: NDORMS

country: United Kingdom

institute: Kennedy Institute of Rheumatology

description:
sscontrol_bm_sthsc_R3
featureCounts.counts.txt
cufflinks.fpkms.txt

data_processing:
Sequence reads were aligned to the mouse genome with Hisat2 (version 2.0.4) using a “genome_trans” index built from the mm10 release of the mouse genome and Ensembl version 83 annotations (two-pass strategy to discover novel splice sites; with parameters: --dta and --score-min L,0.0,-0.2).
Mapped reads were counted using featureCounts (Subread version 1.5.0; Ensembl version 83 annotations; default parameters).
FPKMs were estimated with cuffquant (Cufflinks version 2.2.1; Ensembl version 83 annotations; with parameters:  --multi-read-correct --no-effective-length-correction --max-bundle-frags 2000000 --max-mle-iterations 10000 --frag-bias-correct).
Upper quartile normalised FPKM values were computed using cuffnorm (Cufflinks version 2.2.1; with parameters: --compatible-hits-norm --library-norm-method quartile).
Genome_build: mm10
Supplementary_files_format_and_content: (1) "featureCounts.counts.txt" is a tab-delimited text file containing the table of gene-by-sample read counts computed with the featureCounts algorithm. (2) "cufflinks.fpkms.txt" is a tab-delimited text file containing the table of gene-by-sample upper-quartile normalized FPKMs computed with cuffquant/cuffnorm.

source_name: bone marrow

growth_protocol: Mice were bred and maintained under specific pathogen free conditions in an accredited animal facility at the University of Oxford and the experiments were conducted in accordance with the UK Scientific Procedures Act of 1986 under a Project License (PPL) authorized by the UK Home Office Animal Procedures Committee.

extract_protocol:
Total RNA was isolated using a QIAGEN RNAeasy microkit.
cDNA was prepared using the SMARTer protocol (Clontech) and sequencing libraries prepared using the NEBNext Ultra protocol (NEB).

treatment_protocol: Spondyloarthritis was induced in 8 to 10 week old female SKG mutant mice by injecting curdlan intraperitoneally for 5-6 weeks. Mice were sacrificed and compared with control mice.Bone marrow cells were isolated from fibia and tibia from indicated mice. Indicated stem cell populations were FACS sorted directly into RLT buffer with β-mercaptoethanol and flash frozen on dry ice prior to RNA isolation.

tag: strain

value: BALBC/c

tag: genotype

value: Zap70m1Saka (SKG mutant)

value: steady state

value: healthy

value: bone marrow

value: STHSC


title: m_356

value: 356 min


title: sscontrol_bm_sthsc_R2

description:
sscontrol_bm_sthsc_R2
featureCounts.counts.txt
cufflinks.fpkms.txt

tag: tissue


title: m_340

value: 340 min


title: m_344

value: Neural induction medium

value: 344 min


title: m_348

value: 348 min


title: sscontrol_bm_sthsc_R1

description:
sscontrol_bm_sthsc_R1
featureCounts.counts.txt
cufflinks.fpkms.txt


title: sscontrol_bm_mpp_R2

description:
sscontrol_bm_mpp_R2
featureCounts.counts.txt
cufflinks.fpkms.txt

value: MPP


title: sscontrol_bm_mpp_R1

description:
sscontrol_bm_mpp_R1
featureCounts.counts.txt
cufflinks.fpkms.txt


title: m_352

value: 352 min


title: sscontrol_bm_lthsc_R3

description:
sscontrol_bm_lthsc_R3
featureCounts.counts.txt
cufflinks.fpkms.txt

value: LT-HSC


title: m_336

value: Mouse Epiblast stem cells

value: 336 min


title: m_328

value: 328 min


title: sscontrol_bm_mpp_R3

description:
sscontrol_bm_mpp_R3
featureCounts.counts.txt
cufflinks.fpkms.txt

value: BALBC/c


title: Peritoneal macrophage, WT-lps-

city: shanghai

first: Yaguang

last: Zhang

address: Yueyang road 320, Shanghai, China

institute: CAS, SIBCB

data_processing:
Solexa pipeline version 1.8 (Off-Line Base Caller software, version 1.8) used for basecalling
We used the StringTie software (v1.2.3) to estimate the abundance of the gene level and transcript level, referring to the official database information, then to calculate FPKM the gene or transcript level separately and to find the difference using Ballgown software.
Sequenced reads was filtered through Solexa CHASTITY, and to match to the corresponding reference genome mm9, by Hisat2 software（v2.0.4）
Genome_build: mm9
Supplementary_files_format_and_content: BP_result.xls is for GO Biological Process Classification.
KEGG_MMU00330_ARGININE_AND_PROLINE_METABOLISM.txt is for KEGG GSEA analysis.
All differential FPKM values.xlsx is for FPKM values.

source_name: peritoneal macrophage

extract_protocol:
Total RNA from nonactivated peritoneal macrophages was quantified using a NanoDrop ND-1000 instrument, and 1 to 2 µg of total RNA was used to prepare the sequencing library with the following steps: (1) Total RNA was enriched by oligo (dT) magnetic beads (rRNA removed), and (2) the RNA-Seq library was prepared using the KAPA Stranded RNA-Seq Library Prep Kit (Illumina), which incorporates dUTP into the second cDNA strand and renders the RNA-Seq library strand-specific.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: peritoneal macrophage


title: Peritoneal macrophage, KO-lps-


title: m_332

value: 332 min


title: m_324

value: 324 min


title: m_320

value: 320 min


title: sscontrol_bm_gmp_R3

description:
sscontrol_bm_gmp_R3
featureCounts.counts.txt
cufflinks.fpkms.txt

value: Zap70m1Saka (SKG mutant)

value: steady state

value: healthy

value: bone marrow

value: GMP


title: sscontrol_bm_lthsc_R1

description:
sscontrol_bm_lthsc_R1
featureCounts.counts.txt
cufflinks.fpkms.txt


title: sscontrol_bm_lthsc_R2

description:
sscontrol_bm_lthsc_R2
featureCounts.counts.txt
cufflinks.fpkms.txt


title: sscontrol_bm_gmp_R2

description:
sscontrol_bm_gmp_R2
featureCounts.counts.txt
cufflinks.fpkms.txt


title: m_316

value: Neural induction medium

value: 316 min


title: HEK293_Negative control miRNA mimic

city: Fukuoka

first: Kai

last: Yasukawa

state: Fukuoka

address: 744 Motooka, Nishi-ku

department: Department of Systems Life Sciences

country: Japan

institute: Kyusyu University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v3; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: HEK293, Negative control miRNA mimic

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated from cells using QIAzol Lysis Reagent (Qiagen) and purified using miRNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.


title: sscontrol_bm_gmp_R1

description:
sscontrol_bm_gmp_R1
featureCounts.counts.txt
cufflinks.fpkms.txt


title: m_308

value: 308 min


title: m_312

value: 312 min


title: curdlan_bm_sthsc_R3

description:
curdlan_bm_sthsc_R3
featureCounts.counts.txt
cufflinks.fpkms.txt

value: curdlan (i.p injection)

value: spondyloarthritic

value: STHSC


title: m_296

value: Mouse Epiblast stem cells

value: 296 min


title: m_292

value: 292 min


title: curdlan_bm_sthsc_R2

description:
curdlan_bm_sthsc_R2
featureCounts.counts.txt
cufflinks.fpkms.txt

value: BALBC/c


title: m_300

value: 300 min


title: m_304

value: 304 min


title: m_288

value: 288 min


title: m_284

value: 284 min


title: curdlan_bm_lthsc_R3

description:
curdlan_bm_lthsc_R3
featureCounts.counts.txt
cufflinks.fpkms.txt

value: Zap70m1Saka (SKG mutant)

value: bone marrow

value: LT-HSC


title: curdlan_bm_mpp_R2

description:
curdlan_bm_mpp_R2
featureCounts.counts.txt
cufflinks.fpkms.txt

value: MPP


title: curdlan_bm_mpp_R1

description:
curdlan_bm_mpp_R1
featureCounts.counts.txt
cufflinks.fpkms.txt


title: HEK293_miR-302b mimic

source_name: HEK293, miR-302b mimic


title: m_280

description:
mm10genes.no_mt.ec.tab
mm10genes.no_mt.tpm.rescale.tab

value: Neural induction medium

value: 280 min


title: curdlan_bm_lthsc_R2

description:
curdlan_bm_lthsc_R2
featureCounts.counts.txt
cufflinks.fpkms.txt

value: curdlan (i.p injection)


title: curdlan_bm_lthsc_R1

description:
curdlan_bm_lthsc_R1
featureCounts.counts.txt
cufflinks.fpkms.txt

value: spondyloarthritic


title: curdlan_bm_mpp_R3

description:
curdlan_bm_mpp_R3
featureCounts.counts.txt
cufflinks.fpkms.txt


title: m_276

value: 276 min


title: curdlan_bm_gmp_R3

description:
curdlan_bm_gmp_R3
featureCounts.counts.txt
cufflinks.fpkms.txt

value: GMP


title: m_268

value: Mouse Epiblast stem cells

value: 268 min


title: curdlan_bm_gmp_R1

description:
curdlan_bm_gmp_R1
featureCounts.counts.txt
cufflinks.fpkms.txt

value: BALBC/c


title: curdlan_bm_gmp_R2

description:
curdlan_bm_gmp_R2
featureCounts.counts.txt
cufflinks.fpkms.txt


title: m_264

value: 264 min


title: 16hr_mock_rep4

city: Mohali

first: Hasthi

last: Ram

address: Sector 81

department: Agriculture biotechnology

institute: NABI (National Agri-Food Biotechnology Institute)

data_processing:
The first phase of the data analysis pipeline was the quality control step. In this step, the quality of the raw sequencing data was assessed using the tool FastQC
Bases with bad quality (Phred score <20), over-represented PCR primers and bases with fluctuating GC content identified in this step were pruned using a combination of Cutadapt and Seqtk  tools.
The second phase of quality control was the removal of rRNA reads from raw sequencing data.
For aligning the filtered raw data, we used the standard Arabidopsis genome annotation, TAIR10, and used TopHat tool.
we used the python package HTSeq to count the reads that are aligned to each genomic feature (exon) and to generate gene expression read count matrices. For identifying the deferentially expressed genes from the read count data, we used the R package DESeq2, which models read count data following a negative binomial distribution
Genome_build: Arabidopsis genome annotation, TAIR10
Supplementary_files_format_and_content: .csv file having gene ID and number of counts in tab delimited format

organism: Arabidopsis thaliana

source_name: shoot apical meristem

growth_protocol: Plants were grown on soil in short day conditions for 4-5 weeks before harvesting

extract_protocol:
Rneasy Mini kit (Qiagen) was used according to manufacturer’s instruction for RNA preparation
RNA-Seq Libraries for all the samples were prepared using ‘TruSeq Stranded mRNA Library Prep Kit from Illumina'.

treatment_protocol: Plants were treated with 1 mm IAA+lanolin paste or mcok paste for different time points. About 10 SAM  were quickly harvested and qucik forzen in liquid nitrogen for one biological replicate.

value: mock paste


title: curdlan_bm_sthsc_R1

description:
curdlan_bm_sthsc_R1
featureCounts.counts.txt
cufflinks.fpkms.txt

value: STHSC


title: m_260

value: 260 min


title: m_256

value: 256 min


title: 16hr_mock_rep3


title: 16hr_mock_rep2


title: m_248

value: 248 min


title: m_252

value: 252 min


title: m_244

value: 244 min


title: 16hr_IAA_rep3

value: IAA paste


title: 16hr_mock_rep1


title: m_240

value: Neural induction medium

value: 240 min


title: 16hr_IAA_rep2


title: 12hr_mock_rep3


title: m_232

value: 232 min


title: 12hr_mock_rep2


title: m_272

value: 272 min


title: 16hr_IAA_rep1


title: 12hr_mock_rep1


title: 12hr_IAA_rep4


title: m_224

value: 224 min


title: m_216

value: Mouse Epiblast stem cells

value: 216 min


title: m_212

value: 212 min


title: m_220

value: 220 min


title: 12hr_IAA_rep2


title: 12hr_IAA_rep3


title: m_208

value: 208 min


title: m_204

value: 204 min


title: 4hr_Mock_rep2

value: mock paste


title: m_200

value: 200 min


title: m_196

value: 196 min


title: 4hr_Mock_rep1


title: 4hr_Mock_rep3


title: m_192

value: 192 min


title: m_236

value: 236 min


title: 4hr_IAA_rep2

value: IAA paste


title: 4hr_IAA_rep1


title: m_184

value: Neural induction medium

value: 184 min


title: 4hr_IAA_rep3


title: m_180

value: 180 min